As integral components of eukaryotic genomes, transposable elements could potentially affect the host in many ways. I have recently discovered several novel families of putative transposable elements in the yellow fever mosquito, Aedes aegypti. These include 8 non-LTR retrotransposons that could represent 8 novel families, and 4 novel families of MITE-like transposable elements. These are indications that the non-LTR retrotransposons and MITE-like elements could be the major long and short interspersed repetitive elements in Ae. aegypti. Some of these elements may be non-randomly distributed. furthermore, some of these elements showed associations with genes: The following specific aims will be pursued in this study: 1. Further determine the characteristics, abundance, and diversity of the newly discovered non-LTR retrotransposons and MITE-like elements in Ae. aegypti (Rock strain) 2. Study the distribution and organization of the non-LTR retrotransposons and MITE-like elements in the Ae. aegypti genome (Rock strain) 3. Investigate the distribution of the non-LTR retrotransposons, MITE- like elements, and other repetitive sequences in relation to transcribed genes in Ae. aegypti (Rock strain) 4. Analyze the conservation and polymorphisms of the non-LTR retrotransposons and MITE-like elements in different strains of Ae. aegypti 5. Survey the inter-species distribution of the non-LTR retrotransposons and MITE-like elements Mosquitoes including Ae. aegypti and Anopheles gambiae, are important vectors for many human and animal diseases such as malaria, yellow fever, and dengue fever. Genetic engineering has been one of the focuses of current effort to control these diseases. This study will enhance the understanding of the genetic makeup and organization of the Ae. aegypt genome, and shed light on the relationship between genes and respective elements. It will also provide basis for isolating polymorphic markers that can be used in genetic mapping and population studies, and possibly active elements that can be used as transformation vectors. This study will also help the comparative genomics between Ae. aegypti and An. gambiae relating to transposable elements. These basic genetic information and tools are critical in developing successful and sustainable genetic control strategies.